When you are running antechamber, according to the “help” output, GAFF is the default. So without specifying -at gaff2 you should get the “old” gaff atom types.
antechamber
-at atom type
gaff : the default
Therefore, you should supply the “gaff2” atom type option of you intend to use gaff2. Regarding parmchk, my default is parmchk2 and according to the “help” material, the default here is also “gaff”
parmchk2
-s ff parm set, it is suppressed by "-p" option
1: gaff (the default)
So you should likely define -at 2/gaff2 here as well to ensure that you are using the version.
The tleap script looks correct and I have used gaff2 without issues.
Best regards
// Gustaf
> On 3 Dec 2020, at 02:41, Alexander Izvorski <aizvorski.gmail.com> wrote:
>
> Dear Amber users,
>
> I'm trying to figure out how to use GAFF2 in antechamber/tleap. It seems
> the default for a lot of tools is GAFF (the old version, not GAFF2), and
> the options to switch to GAFF2 consistently are not completely obvious.
> I'm using ambertools-20.9 from conda-forge.
>
> Here's what I have so far:
>
> 1. Run antechamber: no special options needed for GAFF2?
>
> antechamber -i lig_in.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -rn LIG
>
> I noticed that "-at gaff2" is a possible option here - is it needed? If
> that is added, what happens is a bunch of errors when running tleap later,
> "Error! Could not find bond parameter for: ns - ca" and similar, about a
> dozen total for the example molecule, and "Warning! There are missing
> parameters." But the frcmod file doesn't seem to have any errors.
>
> 2. Run parmchk: "-s gaff2" enables GAFF2 here
>
> parmchk2 -i lig.mol2 -f mol2 -o lig.frcmod -s gaff2
>
> 3. Run tleap: source leaprc.gaff2 loads GAFF2
>
> tleap -f tleap.in, where tleap.in is the following file:
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> source leaprc.gaff2
> LIG = loadmol2 lig.mol2
> check LIG
> loadamberparams lig.frcmod
> saveoff LIG lig.lib
> saveamberparm LIG lig.prmtop lig.inpcrd
> quit
>
> This works using sustiva.mol2
> <http://ambermd.org/tutorials/basic/tutorial4b/files/sustiva.mol2> from the
> tutorial <http://ambermd.org/tutorials/basic/tutorial4b/index.html> as the
> input ligand.
>
> Could someone who is familiar with the options for GAFF2 please have a look
> and see if anything is missing from the above?
>
> Best regards,
> Alex
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Received on Thu Dec 03 2020 - 00:30:02 PST
